Refactor `a_summary` #983

edelarua · 2023-06-22T20:45:26Z

Closes #966

Done in this PR:

Refactored a_summary to no longer use create_afun_summary
Deprecated a_compare to reduce replicated code (almost identical to a_summary), added a compare option to a_summary to account for differences between summary and compare
Deprecated create_afun_summary and create_afun_compare which are no longer used
Created new helper function ungroup_stats to ungroup statistics calculated for each level of a factor

github-actions · 2023-06-22T20:52:41Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      62       0  100.00%
R/abnormal_by_marked.R                        52       5  90.38%   115-119
R/abnormal_by_worst_grade_worsen.R           113       3  97.35%   233-235
R/abnormal_by_worst_grade.R                   37       0  100.00%
R/abnormal.R                                  40       0  100.00%
R/analyze_variables.R                        299       4  98.66%   649-652, 936-937
R/analyze_vars_in_cols.R                     113      23  79.65%   164, 188-193, 206, 219-225, 268-274, 305
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        104       5  95.19%   127-131, 243, 365
R/control_incidence_rate.R                    20       8  60.00%   32-35, 38-41
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          47       1  97.87%   63
R/count_missed_doses.R                        31       0  100.00%
R/count_occurrences_by_grade.R                84       6  92.86%   156-158, 161, 176-177
R/count_occurrences.R                         61       1  98.36%   92
R/count_patients_events_in_cols.R             67       1  98.51%   62
R/count_patients_with_event.R                 33       0  100.00%
R/count_patients_with_flags.R                 44       4  90.91%   71-72, 77-78
R/count_values.R                              24       0  100.00%
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 239, 254, 262, 268-269
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            169      40  76.33%   232-263, 323-325, 332, 353-390
R/desctools_binom_diff.R                     663      66  90.05%   55, 90-91, 131-132, 135, 214, 240-249, 288, 290, 310, 314, 318, 322, 378, 381, 384, 387, 448, 456, 468-469, 475-478, 486, 489, 498, 501, 549-550, 552-553, 555-556, 558-559, 629, 641-654, 659, 706, 719, 723
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  47       1  97.87%   60
R/estimate_proportion.R                      199      12  93.97%   75-82, 86, 91, 294, 461, 566
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       2  98.26%   145, 155
R/g_forest.R                                 437      23  94.74%   197, 248-249, 316, 333-334, 339-340, 353, 369, 416, 447, 523, 532, 613-617, 627, 702, 705, 829
R/g_lineplot.R                               199      30  84.92%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 447, 449
R/g_step.R                                    68       1  98.53%   109
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        74       0  100.00%
R/h_biomarkers_subgroups.R                    40       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        65       1  98.46%   91
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/incidence_rate.R                            93       7  92.47%   55-62
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        637      65  89.80%   225-228, 268-303, 312-316, 516, 690-692, 700-702, 727, 734-735, 907, 1096, 1413-1424
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               106       0  100.00%
R/prop_diff_test.R                            88       0  100.00%
R/prop_diff.R                                260      16  93.85%   72-75, 107, 267-274, 413, 473, 578
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   273, 315-317
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   73-74, 129
R/summarize_ancova.R                          95       1  98.95%   180
R/summarize_change.R                          27       0  100.00%
R/summarize_colvars.R                          9       0  100.00%
R/summarize_coxreg.R                         156       2  98.72%   198, 410
R/summarize_glm_count.R                      164       4  97.56%   159, 164, 208, 261
R/summarize_num_patients.R                    74       9  87.84%   103-105, 150-151, 217-222
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   56
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   73       9  87.67%   59-67
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             47       0  100.00%
R/survival_timepoint.R                       116       7  93.97%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                             124       4  96.77%   84, 313, 318, 325
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 346-347
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9241     444  95.20%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  --------
R/analyze_variables.R      +79      +2  -0.43%
R/compare_variables.R      -35       0  -1.21%
R/g_lineplot.R               0      +1  -0.50%
R/summarize_colvars.R       +3       0  +100.00%
R/utils_factor.R           +37      +3  -2.08%
TOTAL                      +84      +6  -0.02%

Results for commit: bfe2840

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

github-actions · 2023-06-22T21:53:12Z

Unit Tests Summary

      1 files   79 suites 56s ⏱️
  752 tests 747 ✔️     5 💤 0 ❌
1 589 runs 996 ✔️ 593 💤 0 ❌

Results for commit 008d5f8.

♻️ This comment has been updated with latest results.

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

shajoezhu · 2023-07-10T14:24:57Z

hey guys, let's deprioritize this PR please after the ocean release. Thanks @edelarua @Melkiades

github-actions · 2023-07-12T01:46:19Z

Code Coverage Summary

Filename                                   Stmts    Miss  Cover    Missing
---------------------------------------  -------  ------  -------  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
R/abnormal_by_baseline.R                      63       0  100.00%
R/abnormal_by_marked.R                        53       5  90.57%   115-119
R/abnormal_by_worst_grade_worsen.R           114       3  97.37%   233-235
R/abnormal_by_worst_grade.R                   38       0  100.00%
R/abnormal.R                                  41       0  100.00%
R/analyze_variables.R                        193       3  98.45%   410, 702-703
R/analyze_vars_in_cols.R                     120      22  81.67%   164, 188-193, 206, 219-225, 276-282
R/combination_function.R                       9       0  100.00%
R/compare_variables.R                        104       5  95.19%   127-131, 243, 369
R/control_incidence_rate.R                    20       8  60.00%   32-35, 38-41
R/control_logistic.R                           7       0  100.00%
R/control_step.R                              23       1  95.65%   58
R/control_survival.R                          15       0  100.00%
R/count_cumulative.R                          48       1  97.92%   63
R/count_missed_doses.R                        32       0  100.00%
R/count_occurrences_by_grade.R                85       6  92.94%   156-158, 161, 176-177
R/count_occurrences.R                         62       1  98.39%   92
R/count_patients_events_in_cols.R             67       1  98.51%   62
R/count_patients_with_event.R                 34       0  100.00%
R/count_patients_with_flags.R                 45       4  91.11%   71-72, 77-78
R/count_values.R                              25       0  100.00%
R/cox_regression_inter.R                     154       0  100.00%
R/cox_regression.R                           161       0  100.00%
R/coxph.R                                    167       7  95.81%   191-195, 239, 254, 262, 268-269
R/d_pkparam.R                                406       0  100.00%
R/decorate_grob.R                            169      40  76.33%   232-263, 323-325, 332, 353-390
R/desctools_binom_diff.R                     663      66  90.05%   52, 87-88, 128-129, 132, 211, 237-246, 285, 287, 307, 311, 315, 319, 375, 378, 381, 384, 445, 453, 465-466, 472-475, 483, 486, 495, 498, 546-547, 549-550, 552-553, 555-556, 626, 638-651, 656, 703, 716, 720
R/df_explicit_na.R                            30       0  100.00%
R/estimate_multinomial_rsp.R                  48       1  97.92%   60
R/estimate_proportion.R                      200      12  94.00%   75-82, 86, 91, 296, 463, 568
R/fit_rsp_step.R                              36       0  100.00%
R/fit_survival_step.R                         36       0  100.00%
R/formatting_functions.R                     115       2  98.26%   145, 155
R/g_forest.R                                 437      23  94.74%   197, 248-249, 316, 333-334, 339-340, 353, 369, 416, 447, 523, 532, 613-617, 627, 702, 705, 829
R/g_lineplot.R                               199      30  84.92%   160, 173, 201, 227-230, 307-314, 332-333, 339-349, 441, 447, 449
R/g_step.R                                    68       1  98.53%   109
R/g_waterfall.R                               47       0  100.00%
R/h_adsl_adlb_merge_using_worst_flag.R        73       0  100.00%
R/h_biomarkers_subgroups.R                    40       0  100.00%
R/h_cox_regression.R                         110       0  100.00%
R/h_logistic_regression.R                    468       3  99.36%   206-207, 276
R/h_map_for_count_abnormal.R                  54       0  100.00%
R/h_pkparam_sort.R                            15       0  100.00%
R/h_response_biomarkers_subgroups.R           75       0  100.00%
R/h_response_subgroups.R                     171      12  92.98%   257-270
R/h_stack_by_baskets.R                        64       1  98.44%   89
R/h_step.R                                   180       0  100.00%
R/h_survival_biomarkers_subgroups.R           79       0  100.00%
R/h_survival_duration_subgroups.R            200      12  94.00%   259-271
R/incidence_rate.R                            94       7  92.55%   53-60
R/individual_patient_plot.R                  133       0  100.00%
R/kaplan_meier_plot.R                        646      64  90.09%   226-229, 269-304, 313-317, 517, 704-706, 714-716, 748-749, 921, 1110, 1427-1438
R/logistic_regression.R                      101       0  100.00%
R/missing_data.R                              21       3  85.71%   32, 66, 76
R/odds_ratio.R                               107       0  100.00%
R/prop_diff_test.R                            89       0  100.00%
R/prop_diff.R                                261      16  93.87%   72-75, 107, 269-276, 415, 475, 580
R/prune_occurrences.R                         57      10  82.46%   138-142, 188-192
R/response_biomarkers_subgroups.R             60       0  100.00%
R/response_subgroups.R                       165       4  97.58%   266, 308-310
R/rtables_access.R                            38       4  89.47%   159-162
R/score_occurrences.R                         20       1  95.00%   124
R/split_cols_by_groups.R                      49       0  100.00%
R/stat.R                                      47       3  93.62%   73-74, 129
R/summarize_ancova.R                          96       1  98.96%   180
R/summarize_change.R                          28       0  100.00%
R/summarize_colvars.R                          9       0  100.00%
R/summarize_coxreg.R                         165       2  98.79%   198, 420
R/summarize_glm_count.R                      165       4  97.58%   158, 163, 207, 260
R/summarize_num_patients.R                    75       9  88.00%   103-105, 150-151, 218-223
R/summarize_patients_exposure_in_cols.R       97       1  98.97%   56
R/summary_stats.R                            101       0  100.00%
R/survival_biomarkers_subgroups.R             60       0  100.00%
R/survival_coxph_pairwise.R                   74       9  87.84%   59-67
R/survival_duration_subgroups.R              172       0  100.00%
R/survival_time.R                             48       0  100.00%
R/survival_timepoint.R                       118       7  94.07%   126-132
R/utils_checkmate.R                           68       0  100.00%
R/utils_factor.R                             107       1  99.07%   84
R/utils_grid.R                               111       5  95.50%   149, 258-264
R/utils_rtables.R                             86       7  91.86%   24, 31-35, 346-347
R/utils.R                                    137      10  92.70%   92, 94, 98, 118, 121, 124, 128, 137-138, 311
TOTAL                                       9268     438  95.27%

Diff against main

Filename                 Stmts    Miss  Cover
---------------------  -------  ------  --------
R/analyze_variables.R      -27      +1  -0.65%
R/compare_variables.R      -35       0  -1.21%
R/g_lineplot.R               0      +1  -0.50%
R/summarize_colvars.R       +3       0  +100.00%
R/summary_stats.R         +101       0  +100.00%
R/utils_factor.R           +20       0  +0.21%
TOTAL                      +62      +2  +0.01%

Results for commit: ad19874

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

NAMESPACE

R/analyze_variables.R

R/utils_factor.R

Melkiades · 2023-07-14T16:13:53Z

hey guys, let's deprioritize this PR please after the ocean release. Thanks @edelarua @Melkiades

Emily and I went through it together and it seems ready to go in. I will double-check downstream effects but Emily already did check it. Let us know what you think, it is fine to wait after ocean release

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

Melkiades

@shajoezhu we already reviewed this last week. It was only waiting for the release. It is good to go for me ;)

shajoezhu · 2023-07-28T11:18:41Z

Thanks @Melkiades . This is quite substantial change. I would like to request the chevron team to run a UAT on this please. @clarkliming @BFalquet

shajoezhu · 2023-07-28T15:57:48Z

Thanks a lot guys! @edelarua @Melkiades . seems there will be changes needed downstream, let's work with @BFalquet and @clarkliming , and use staged.deps to track some of the changes. also in tlg-c. Thanks a lot!

clarkliming · 2023-08-05T13:39:05Z

Thanks a lot guys! @edelarua @Melkiades . seems there will be changes needed downstream, let's work with @BFalquet and @clarkliming , and use staged.deps to track some of the changes. also in tlg-c. Thanks a lot!

@BFalquet please hold on the update at the moment. We need to deliver another release to autovalidator. And staged.dependency will pull the latest changes and there will be errors in the actions and daily checks. We just make sure R cmd check works on our local branch at the moment.

NEWS.md

R/analyze_variables.R

edelarua added 13 commits June 14, 2023 19:13

Refactor a_summary, deprecate create_afun_summary

9aa6358

Refactor a_compare, deprecate create_afun_compare

c059658

Update pkgdown, remove browser calls

6df46b9

Fix extract_by_name

cf35bce

Fix NA handling

c332906

Merge branch 'main' into 966_refactor_a_summary@main

9a2d615

Modularize

f2cd062

Remove duplication (a_compare)

6e89c20

Add workaround for all-NA rows

c0c783a

Add tests, fix lint, update NEWS

eb62629

Improve code

825c36f

Merge branch 'main' into 966_refactor_a_summary@main

0b31e3f

Update stale snapshots

ec7a1a3

edelarua added the sme label Jun 22, 2023

edelarua and others added 2 commits June 22, 2023 20:45

Merge ec7a1a3 into d9c27e0

33e6671

[skip actions] Restyle files

65572ff

edelarua and others added 6 commits June 22, 2023 17:05

Add test, update NEWS

2a870c2

Merge 2a870c2 into d9c27e0

9ae74bb

[skip actions] Restyle files

b66be67

Update deprecated functions, roxygen

c23aeab

Update WORDLIST

11d8696

Fix checks

93fc5e1

edelarua linked an issue Jun 22, 2023 that may be closed by this pull request

In some cases using summarize_vars and add_overall_col leads to issue . #292

Closed

2 tasks

Melkiades self-requested a review June 23, 2023 13:58

This was referenced Jun 23, 2023

prep for v0.8.4 #978

Closed

prep for release v0.9.0 #990

Closed

clarkliming mentioned this pull request Jun 29, 2023

allow more statistics in cfbt01 template insightsengineering/chevron#552

Merged

Merge branch 'main' into 966_refactor_a_summary@main

77ccdc5

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

edelarua and others added 4 commits July 4, 2023 21:03

Update WORDLIST

2953a5d

roxygen examples too wide

10d4794

Merge branch 'main' into 966_refactor_a_summary@main

5d602bc

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

Merge branch 'main' into 966_refactor_a_summary@main

4ac191b

shajoezhu added the blocked label Jul 10, 2023

Separate files for summary funs, internal afun helper

c8b430d

Melkiades reviewed Jul 14, 2023

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Melkiades reviewed Jul 14, 2023

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Melkiades reviewed Jul 14, 2023

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edelarua added 3 commits July 14, 2023 20:18

Clean up a_summary and ungroup_stats, export a_compare

28b803d

Update NEWS

d0e341c

Fix tests

62c7990

edelarua removed the blocked label Jul 21, 2023

edelarua and others added 2 commits July 21, 2023 15:43

Organize tests

87b738a

Merge branch 'main' into 966_refactor_a_summary@main

4814842

Signed-off-by: Davide Garolini <davide.garolini@roche.com>

Melkiades approved these changes Jul 28, 2023

View reviewed changes

Melkiades and others added 2 commits August 4, 2023 12:17

Merge branch 'main' into 966_refactor_a_summary@main

a013935

[skip actions] Roxygen Man Pages Auto Update

3d99098

Melkiades added 2 commits August 7, 2023 09:33

Merge branch 'main' into 966_refactor_a_summary@main

0c2a850

Merge branch 'main' into 966_refactor_a_summary@main

008d5f8

Melkiades merged commit 25b06d4 into main Aug 16, 2023

Melkiades deleted the 966_refactor_a_summary@main branch August 16, 2023 08:08

pawelru reviewed Aug 16, 2023

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Refactor `a_summary` #983

Refactor `a_summary` #983

edelarua commented Jun 22, 2023 •

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shajoezhu commented Jul 10, 2023

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Melkiades commented Jul 14, 2023

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shajoezhu commented Jul 28, 2023

shajoezhu commented Jul 28, 2023

clarkliming commented Aug 5, 2023

Refactor a_summary #983

Refactor a_summary #983

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shajoezhu commented Jul 28, 2023

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clarkliming commented Aug 5, 2023

Refactor `a_summary` #983

Refactor `a_summary` #983

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